Package: pareg 1.9.0

Kim Philipp Jablonski

pareg: Pathway enrichment using a regularized regression approach

Compute pathway enrichment scores while accounting for term-term relations. This package uses a regularized multiple linear regression to regress differential expression p-values obtained from multi-condition experiments on a pathway membership matrix. By doing so, it is able to incorporate additional biological knowledge into the enrichment analysis and to estimate pathway enrichment scores more robustly.

Authors:Kim Philipp Jablonski [aut, cre]

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pareg.pdf |pareg.html✨
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NEWS

# Install 'pareg' in R:

install.packages('pareg', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/cbg-ethz/pareg/issues

Datasets:

pathway_similarities - Collection of pathway similarity matrices.

On BioConductor:pareg-1.9.0(bioc 3.20)pareg-1.8.0(bioc 3.19)

bioconductor-package

21 exports 0.71 score 196 dependencies

Last updated 2 months agofrom:c9db169b58

Exports:as_dense_sim as_enrichplot_object bernoulli beta beta_phi_lm beta_phi_var cluster_apply compute_term_similarities create_model_df cv_edgenet edgenet family gaussian generate_similarity_matrix jaccard overlap_coefficient pareg pareg_env plot_pareg_with_args similarity_sample transform_y

Dependencies:AnnotationDbi askpass backports base64enc basilisk basilisk.utils BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 blob brew brio bslib cachem callr cli clipr codetools colorspace commonmark config cowplot cpp11 crayon credentials curl data.table DBI desc devtools diffobj digest dir.expiry doFuture doRNG DOSE downlit dplyr ellipsis evaluate fansi farver fastmap fastmatch fgsea filelock fontawesome foreach formatR fs futile.logger futile.options future future.apply generics GenomeInfoDb GenomeInfoDbData gert ggforce ggplot2 ggraph ggrepel gh gitcreds globals glue GO.db GOSemSim graphlayouts gridExtra gtable HDO.db here highr hms htmltools htmlwidgets httpuv httr httr2 igraph ini IRanges isoband iterators jquerylib jsonlite KEGGREST keras knitr labeling lambda.r later lattice lifecycle listenv logger magrittr MASS Matrix memoise mgcv mime miniUI munsell nlme nloptr openssl parallelly pillar pkgbuild pkgconfig pkgdown pkgload plogr plyr png polyclip praise prettyunits processx profvis progress promises proxy ps purrr qvalue R6 ragg rappdirs rcmdcheck RColorBrewer Rcpp RcppArmadillo RcppEigen RcppTOML rematch2 remotes reshape2 reticulate rlang rmarkdown rngtools roxygen2 rprojroot RSQLite rstudioapi rversions S4Vectors sass scales sessioninfo shiny snow sourcetools stringi stringr sys systemfonts tensorflow testthat textshaping tfautograph tfprobability tfruns tibble tidygraph tidyr tidyselect tinytex tweenr UCSC.utils urlchecker usethis utf8 vctrs viridis viridisLite waldo whisker withr xfun xml2 xopen xtable XVector yaml yulab.utils zeallot zip zlibbioc

Get started

Kim Philipp Jablonski

Rendered frompareg.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2022-03-22
Started: 2021-06-01

Pathway similarities

Kim Philipp Jablonski

Rendered frompathway_similarities.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2022-04-12
Started: 2022-03-22

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Convert matrices.	as_dense_sim
Convert object of class 'pareg' to class 'enrichResult'.	as_enrichplot_object
as.data.frame for an object of class 'pareg'.	as.data.frame.pareg
Parallelize function calls on LSF cluster.	cluster_apply
Term similarity computation.	compute_term_similarities
Create design matrix.	create_model_df
Find the optimal shrinkage parameters for edgenet	cv_edgenet cv_edgenet,matrix,matrix-method cv_edgenet,matrix,numeric-method
Fit a graph-regularized linear regression model using edge-based regularization. Adapted from https://github.com/dirmeier/netReg.	edgenet edgenet,matrix,matrix-method edgenet,matrix,numeric-method
Family objects for models	bernoulli beta beta_phi_lm beta_phi_var family gaussian
Similarity matrix generation.	generate_similarity_matrix
Jaccard similarity.	jaccard
Overlap coefficient.	overlap_coefficient
Pathway enrichment using a regularized regression approach.	pareg
Conda environment definition.	pareg_env
Collection of pathway similarity matrices.	pathway_similarities
Plot result of enrichment computation.	plot_pareg_with_args
Plot pareg object.	plot.pareg
Sample elements based on similarity structure.	similarity_sample
Transform vector from [0, 1] to (0, 1).	transform_y

Package: pareg 1.9.0

pareg: Pathway enrichment using a regularized regression approach

Get started

Pathway similarities

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)